Acta Phys. -Chim. Sin. ›› 2013, Vol. 29 ›› Issue (04): 843-848.doi: 10.3866/PKU.WHXB201301183

• BIOPHYSICAL CHEMISTRY • Previous Articles     Next Articles

Molecular Dynamics Simulations of the Unbinding of Phenylsulfonamide from Carbonic Anhydrase II

SUN Wei-Qi1,3, ZHANG Ji-Long2, ZHENG Qing-Chuan2, SUN Zhi-Wei1,4, ZHANG Hong-Xing2   

  1. 1 School of Public Health, Jilin University, Changchun 130021, P. R. China;
    2 State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, P. R. China;
    3 School of Public Health, Beihua University, Jilin 132013, P. R. China;
    4 School of Public Health and Family Medicine, Capital Medical University, Beijing 100069, P. R. China
  • Received:2012-11-08 Revised:2013-01-15 Published:2013-03-25
  • Supported by:

    The project was supported by the National Natural Science Foundation of China (21273095, 20903045, 21203072), Specialized Research Fund for the Doctoral Program of Higher Education, China (20070183046), and Specialized Fund for the Basic Research of Jilin University, China (201003044).


Molecular dynamics (MD) simulations and free energy calculations were integrated to investigate substrate-enzyme dynamic interactions during the unbinding of phenylsulfonamide from carbonic anhydrase II (CA II). The potential of mean force (PMF) along the unbinding pathway shows that a special ligand-binding state exists, and the electrostatic interaction dominates the ligand?s binding with CA II. The analysis of trajectories reveals that, apart from the zinc ion, the key residues in the unbinding pathway, Leu198, Thr199, and Thr200, prevent the substrate?s unbinding from the enzyme by hydrogen bonding with the sulfanilamide group of the substrate. The present results are of direct significance for the in-depth understanding of the sulfonamide-CA II binding process and related drug design.

Key words: Molecular dynamics simulation, Free energy, Phenylsulfonamide, Carbonic anhydrase II, Substrate’s binding


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